Hi I Used this command:
speedseq align \
-o 5863-DD-3
-R "@rg\tID:5863-DD-3\tSM:5863-DD-3\tLB:ILLUMINA"
assembly38.fasta
5863-DD-3-R1_001.fastq.gz
5863-DD-3-R2_001.fastq.gz
I have the discordant and splitters bams but I do not have the main bam file. Could you please help me with this.
Thank you